[BioC] Minor allele frequency comparison

[Scott Harding]

Hi all,

    We are using two methods to identify SNPs. One is based on
resequencing the genome and aligning the reads to the sequenced genome
to identify SNPs (data available for 44 individuals). Another is based
on  SNP array with selected loci (30000 loci, 870 individuals). I want
to compare the results from the resequencing based minor allele
frequency and Array based minor allele frequency. What statistical
test should I use?

My table looks like



Chromosome           position               Major/minor
Resequencing                 SNP array


chromosome 1         198432                 C/T
  75/13                             1460/280
chromosome 1         14282752             A/G
69/19                             1380/360
chromosome 1          595434                T/G
  83/5                               1680/60


I really appreciate any guidance.

Thanks

Scott